Acronis Backup software may conflict with software that encrypts files or partition structure
Acronis Backup software may fail to back up or restore partitions or files encrypted by specialized software.
The following situations can occur:
Acronis Backup software can always create a raw (sector-by-sector) backup of an encrypted partition when booted from Acronis Bootable Rescue Media. See also Creating a Sector-By-Sector Backup with Acronis Products.
If the encryption key is based on the hard drive or some hardware serial numbers, a sector-by-sector copy may not work as expected. The best solution will then be to create the backup in Windows. Then, when restoring it, do it as you would do it normally. The only difference is that after the restore you will need to rebuild the MBR. See Restoring Windows Boot Loader Manually.